What you are missing is the fact that the current through your resistor is controlled not only by the resistance of your resistor but the circuit elements of a complete electrical circuit of which your resistor is one part.

Your resistor not only has an effect on the current passing through it but also the currents passing through other circuit elements to which it is connected.
In the end as there is no source or sink of charge within your resistor, the current entering your resistor coming from the circuit to which it is connected to is equal to the current leaving the resistor and that current is going into the circuit to which your resistor is connected to.

If the current is larger more charge flows through the resistor per second.

What you are missing is the fact that the current through your resistor is controlled not only by the resistance of your resistor but the circuit elements of a complete electrical circuit of which your resistor is one part.

Your resistor not only has an effect on the current passing through it but also the currents passing through other circuit elements to which it is connected.
In the end as there is no source or sink of charge within your resistor, the current entering your resistor coming from the circuit to which it is connected to is equal to the current leaving the resistor and that current is going into the circuit to which your resistor is connected to.